SMTL ID : 4zwe.5 (4 other biounits)

Crystal structure of the dGTP-bound catalytic core of SAMHD1 T592V mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

homo-dimer

Ligands

6 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)(Covalent)

DGT.1: 17 residues within 4Å: Chain A: Q.37, L.38, R.52, R.94, N.95, H.98, H.103, H.121, D.199, K.200, Y.203, D.207, R.254, H.258, Y.262, Q.263 Ligands: MG.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.262 Hydrogen bonds: A:Q.37, A:R.52, A:D.199, A:Y.203, A:Q.263, A:Q.263 Salt bridges: A:R.52, A:R.94, A:H.98, A:H.103, A:H.103, A:H.121, A:H.121, A:K.200, A:R.254 pi-Cation interactions: A:H.103 DGT.4: 10 residues within 4Å: Chain A: K.4, V.5, I.6, V.21, I.24, D.25, Q.30, R.33, F.53 Ligands: MG.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.6 Hydrogen bonds: A:Q.30, A:R.33 Salt bridges: A:K.4, A:K.4, A:K.4, A:D.25 DGT.5: 15 residues within 4Å: Chain A: R.221, F.225, R.240, K.242, N.246, K.411 Chain B: V.44, F.45, G.212, I.213, R.260, H.264, K.265, V.266 Ligands: DGT.9 17 PLIP interactions: 10 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:R.221, A:N.246, B:G.212 Salt bridges: A:R.221, A:R.240, A:K.242, A:K.242, A:K.242, A:K.411, B:H.264, B:H.264, B:K.265, B:K.265 pi-Cation interactions: A:R.221, A:R.221 Hydrophobic interactions: B:V.44, B:F.45 DGT.7: 13 residues within 4Å: Chain A: V.44, F.45, I.213, R.260, H.264, K.265, V.266 Chain B: R.221, F.225, R.240, K.242, N.246, K.411 18 PLIP interactions: 11 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:D.218, B:R.221, B:N.246 Salt bridges: B:R.221, B:R.240, B:K.242, B:K.242, B:K.242, B:K.411, A:H.264, A:H.264, A:K.265, A:K.265, A:K.265 pi-Cation interactions: B:R.221, B:R.221 Hydrophobic interactions: A:V.44, A:F.45 DGT.8: 20 residues within 4Å: Chain B: Q.37, L.38, G.39, R.52, H.55, R.94, N.95, H.98, F.101, H.103, H.121, D.199, K.200, Y.203, D.207, R.254, H.258, Y.262, Q.263, D.271 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Y.262 Hydrogen bonds: B:Q.37, B:R.52, B:H.103, B:Q.263 Salt bridges: B:R.52, B:R.94, B:R.94, B:H.98, B:H.103, B:H.103, B:H.121, B:K.200, B:K.200, B:R.254, B:D.271 pi-Stacking: B:H.103 DGT.9: 7 residues within 4Å: Chain A: K.411 Chain B: Y.43, V.44, V.266, R.339, K.343 Ligands: DGT.5 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.339 Salt bridges: B:R.339, B:K.343, B:K.343, A:K.411, A:K.411 pi-Cation interactions: B:R.339

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: R.94, K.200 Ligands: DGT.1 No protein-ligand interaction detected (PLIP) MG.3: 2 residues within 4Å: Chain A: K.4 Ligands: DGT.4 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain B: K.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tang, C. et al., Impaired dNTPase Activity of SAMHD1 by Phosphomimetic Mutation of Thr-592. J.Biol.Chem. (2015)

Release Date

2015-09-02

Peptides

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

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